Xinyu Li1, Wei Zhang2, Jianming Zhang3, Guang Li1. 1. State Key Laboratory of Industrial Control Technology, Institute of Cyber-Systems and Control, Zhejiang University, Zheda Road, 310027, Hangzhou, China. 2. State Key Laboratory of Industrial Control Technology, Institute of Cyber-Systems and Control, Zhejiang University, Zheda Road, 310027, Hangzhou, China. zhangweicse@zju.edu.cn. 3. State Key Laboratory of Industrial Control Technology, Institute of Cyber-Systems and Control, Zhejiang University, Zheda Road, 310027, Hangzhou, China. ncsl@zju.edu.cn.
Abstract
BACKGROUND: Given expression data, gene regulatory network(GRN) inference approaches try to determine regulatory relations. However, current inference methods ignore the inherent topological characters of GRN to some extent, leading to structures that lack clear biological explanation. To increase the biophysical meanings of inferred networks, this study performed data-driven module detection before network inference. Gene modules were identified by decomposition-based methods. RESULTS: ICA-decomposition based module detection methods have been used to detect functional modules directly from transcriptomic data. Experiments about time-series expression, curated and scRNA-seq datasets suggested that the advantages of the proposed ModularBoost method over established methods, especially in the efficiency and accuracy. For scRNA-seq datasets, the ModularBoost method outperformed other candidate inference algorithms. CONCLUSIONS: As a complicated task, GRN inference can be decomposed into several tasks of reduced complexity. Using identified gene modules as topological constraints, the initial inference problem can be accomplished by inferring intra-modular and inter-modular interactions respectively. Experimental outcomes suggest that the proposed ModularBoost method can improve the accuracy and efficiency of inference algorithms by introducing topological constraints.
BACKGROUND: Given expression data, gene regulatory network(GRN) inference approaches try to determine regulatory relations. However, current inference methods ignore the inherent topological characters of GRN to some extent, leading to structures that lack clear biological explanation. To increase the biophysical meanings of inferred networks, this study performed data-driven module detection before network inference. Gene modules were identified by decomposition-based methods. RESULTS: ICA-decomposition based module detection methods have been used to detect functional modules directly from transcriptomic data. Experiments about time-series expression, curated and scRNA-seq datasets suggested that the advantages of the proposed ModularBoost method over established methods, especially in the efficiency and accuracy. For scRNA-seq datasets, the ModularBoost method outperformed other candidate inference algorithms. CONCLUSIONS: As a complicated task, GRN inference can be decomposed into several tasks of reduced complexity. Using identified gene modules as topological constraints, the initial inference problem can be accomplished by inferring intra-modular and inter-modular interactions respectively. Experimental outcomes suggest that the proposed ModularBoost method can improve the accuracy and efficiency of inference algorithms by introducing topological constraints.
Entities:
Keywords:
GRNBoost2; Gene module Decomposition; Linear regression; Regulatory network inference
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